Fermented foods are produced through controlled microbial growth — but how do industry professionals manage those complex microorganisms? Three panelists, each with experience in a different field and at a different scale — restaurant chef, artisanal cheesemaker and commercial food producer — shared their insights during a TFA webinar, Managing Fermented Food Microbes to Control Quality

“Producers of fermented foods rely on microbial communities or what we often call microbiomes, these collections of bacteria yeasts and sometimes even molds to make these delicious products that we all enjoy,” says Ben Wolfe, PhD, associate professor at Tufts University, who moderator the webinar along with Maria Marco, PhD, professor at University of California, Davis (both are TFA Advisory Board members). 

Wolfe continued: “Fermenters use these microbial communities every day right, they’re working with them in crocks of kimchi and sauerkraut, they’re working with them in a vat of milk as it’s gone from milk to cheese, but yet most of these microbial communities are invisible. We’re relying on these communities that we rarely can actually see or know in great detail, and so it’s this really interesting challenge of how do you manage these invisible microbial communities to consistently make delicious fermented foods.”

Three panelists joined Wolfe and Marco: Cortney Burns (chef, author and current consultant at Blue Hill at Stone Barns in New York, a farmstead restaurant), Mateo Kehler (founder and cheesemaker at Jasper Hill in Vermont, a dairy farm and creamery) and Olivia Slaugh (quality assurance manager at wildbrine | wildcreamery in California, producers of fermented vegetables and plant-based dairy). 

Fermentation mishaps are not the same for producers because “each kitchen is different, each processing facility, each packaging facility, you really have to tune in to what is happening and understand the nuance within a site,” Marco notes. “Informed trial and error” is important. 

The three agreed that part of the joy of working in the culinary world is creating, and mistakes are part of that process.

“We have learned a lot over the years and never by doing anything right, we’ve learned everything we know by making mistakes,” says Kehler. 

One season at Jasper Hill, aspergillus molds colonized on the rinds of hard cheeses, spoiling them. The cheesemakers discovered that there had been a problem early on as the rind developed. They corrected this issue by washing the cheese more aggressively and putting it immediately into the cellar.

“For the record, I’ve had so many things go wrong,” Burns says. A koji that failed because a heating sensor moved, ferments that turned soft because the air conditioning shut off or a water kefir that became too thick when the ferment time was off. “[Microbes are] alive, so it’s a constant conversation, it’s a relationship really that we’re having with each and every one on a different level, and some of these relationships fall to the wayside or we forget about them or they don’t get the attention they need.”

Burns continues: “All these little safeguards need to be put in place in order for us to have continual success with what we’re doing, but we always learn from it. We move the sensor, we drop the temperature, we leave things for a little bit longer. That’s how we end up manipulating them, it’s just creating an environment that we know they’re going to thrive in.”

Slaugh distinguishes between what she calls “intended microbiology” — the microbes that will benefit the food you’re creating — and “unintended microbiology” — packaging defects, spoilage organisms or a contamination event. 

Slaugh says one of the benefits of working with ferments at a large scale at wildbrine is the cost of routine microbiological analysis is lower. But a mistake is stressful. She recounted a time when thousands of pounds of food needed to be thrown out because of a contaminant in packaging from an ice supplier.

“Despite the fact that the manufacturer was sending us a food-grade or in some cases a medical-grade ingredient, the container does not have the same level of sanitation, so you can’t really take these things for granted,” Slaugh says. 

Her recommendations include supplier oversight, a quality assurance person that can track defects and sample the product throughout fermentation and a detailed process flow diagram. That document, Slaugh advises, should go far beyond what producers use to comply with government food regulations. It should include minutiae like what scissors are used to cut open ingredient bags and the process for employees to change their gloves. 

“I think this is just an incredible time to be in fermented foods,” Kehler adds. “There’s this moment now where you have the arrival of technology. The way I described being a cheesemaker when I started making cheese almost 20 years ago was it was like being a god, except you’re blind and dumb. You’re unleashing these universes of life and then wiping them out and you couldn’t see them, you could see the impacts of your actions, but you may or may not have control. What’s happened since we started making cheese is now the technology has enabled us to actually see what’s happening. I think it’s this groundbreaking moment, we have the acceleration of knowledge. We’re living in this moment where we can start to understand the things that previously could only be intuited.”

A diet high in fermented foods increases microbiome diversity, lowers inflammation, and improves immune response, according to researchers at Stanford University’s School of Medicine.The groundbreaking results were published in the journal Cell.

In the clinical trial, healthy individuals were fed for 10 weeks, a diet either high in fermented foods and beverages or high in fiber. The fermented diet — which included yogurt, kefir, cottage cheese, kimchi, kombucha, fermented veggies and fermented veggie broth — led to an increase in overall microbial diversity, with stronger effects from larger servings.

“This is a stunning finding,” says Justin Sonnenburg, PhD, an associate professor of microbiology and immunology at Stanford. “It provides one of the first examples of how a simple change in diet can reproducibly remodel the microbiota across a cohort of healthy adults.”

Researchers were particularly pleased to see participants in the fermented foods diet showed less activation in four types of immune cells. There was a decrease in the levels of 19 inflammatory proteins, including interleukin 6, which is linked to rheumatoid arthritis, Type 2 diabetes and chronic stress. 

“Microbiota-targeted diets can change immune status, providing a promising avenue for decreasing inflammation in healthy adults,” says Christopher Gardner, PhD, the Rehnborg Farquhar Professor and director of nutrition studies at the Stanford Prevention Research Center. “This finding was consistent across all participants in the study who were assigned to the higher fermented food group.”

Microbiota Stability vs. Diversity

Continues a press release from Stanford Medicine News Center: By contrast, none of the 19 inflammatory proteins decreased in participants assigned to a high-fiber diet rich in legumes, seeds, whole grains, nuts, vegetables and fruits. On average, the diversity of their gut microbes also remained stable. 

“We expected high fiber to have a more universally beneficial effect and increase microbiota diversity,” said Erica Sonnenburg, PhD, a senior research scientist at Stanford in basic life sciences, microbiology and immunology. “The data suggest that increased fiber intake alone over a short time period is insufficient to increase microbiota diversity.”

Justin and Erica Sonnenburg and Christopher Gardner are co-authors of the study. The lead authors are Hannah Wastyk, a PhD student in bioengineering, and former postdoctoral scholar Gabriela Fragiadakis, PhD, now an assistant professor of medicine at UC-San Francisco.

A wide body of evidence has demonstrated that diet shapes the gut microbiome which, in turn, can affect the immune system and overall health. According to Gardner, low microbiome diversity has been linked to obesity and diabetes.

“We wanted to conduct a proof-of-concept study that could test whether microbiota-targeted food could be an avenue for combatting the overwhelming rise in chronic inflammatory diseases,” Gardner said.

The researchers focused on fiber and fermented foods due to previous reports of their potential health benefits. High-fiber diets have been associated with lower rates of mortality. Fermented foods are thought to help with weight maintenance and may decrease the risk of diabetes, cancer and cardiovascular disease.

The researchers analyzed blood and stool samples collected during a three-week pre-trial period, the 10 weeks of the diet, and a four-week period after the diet when the participants ate as they chose.

The findings paint a nuanced picture of the influence of diet on gut microbes and immune status. Those who increased their consumption of fermented foods showed effects consistent with prior research showing that short-term changes in diet can rapidly alter the gut microbiome. The limited changes in the microbiome for the high-fiber group dovetailed with previous reports of the resilience of the human microbiome over short time periods.

Designing a suite of dietary and microbial strategies

The results also showed that greater fiber intake led to more carbohydrates in stool samples, pointing to incomplete fiber degradation by gut microbes. These findings are consistent with research suggesting that the microbiome of a person living in the industrialized world is depleted of fiber-degrading microbes.

“It is possible that a longer intervention would have allowed for the microbiota to adequately adapt to the increase in fiber consumption,” Erica Sonnenburg said. “Alternatively, the deliberate introduction of fiber-consuming microbes may be required to increase the microbiota’s capacity to break down the carbohydrates.”

In addition to exploring these possibilities, the researchers plan to conduct studies in mice to investigate the molecular mechanisms by which diets alter the microbiome and reduce inflammatory proteins. They also aim to test whether high-fiber and fermented foods synergize to influence the microbiome and immune system of humans. Another goal is to examine whether the consumption of fermented foods decreases inflammation or improves other health markers in patients with immunological and metabolic diseases, in pregnant women, or in older individuals.

“There are many more ways to target the microbiome with food and supplements, and we hope to continue to investigate how different diets, probiotics and prebiotics impact the microbiome and health in different groups,” Justin Sonnenburg said.

Other Stanford co-authors are Dalia Perelman, health educator; former graduate students Dylan Dahan, PhD, and Carlos Gonzalez, PhD; graduate student Bryan Merrill; former research assistant Madeline Topf; postdoctoral scholars William Van Treuren, PhD, and Shuo Han, PhD; Jennifer Robinson, PhD, administrative director of the Community Health and Prevention Research Master’s Program and program manager of the Nutrition Studies Group; and Joshua Elias, PhD.

Researchers from the nonprofit research center Chan-Zuckerberg Biohub also contributed to the study. Here’s the complete press release from Stanford Medicine News Center.

Vegan Cheese Matures

Vegan cheese makers are “pushing the limits of those fermentations to create … flavors and textures I’d previously thought impossible,” writes The New York Times food columnist Tejal Rao. She says the “new generation” of vegan cheese is surprisingly tastier than the bland, starchy, mass-produced vegan cheese of the early 2000s. 

Missing from those first versions of vegan cheese: fermentation, a key to creating flavor. Vegan cheese now is also aged and ripened like dairy cheese to develop flavors and textures.

The microbes used to give cheeses like Gouda and Brie their distinct flavors are also critical. Vegan  cheese cultures are now readily available. Aaron Bullock and Ian Marin (pictured), founders of Misha’s Kind Foods, work with proprietary cultures to create cream cheese and ricotta made from cashew milk.

Read more (The New York Times)

By August, any manufacturer labeling their fermented or hydrolyzed foods or ingredients “gluten-free” must prove that they contain no gluten, have never been through a process to remove gluten, all gluten cross-contact has been eliminated and there are measures in place to prevent gluten contamination in production.

The FDA list includes these foods: cheese, yogurt, vinegar, sauerkraut, pickles, green olives, beers, wine and hydrolyzed plant proteins. This category would also include food derived from fermented or hydrolyzed ingredients, such as chocolate made from fermented cocoa beans or a snack using olives.

Read more (JD Supra Legal News

Why do we treat cheese like a guilty pleasure when studies have shown time and again that cheese can be good for you? An article in Wired sheds light on how cheese gained its designation as a villain in the food pyramid. One key element is how many Americans ate in the ‘80s and ‘90s, layering pizza and pasta with heavily-processed cheese.

The article reads: “In the case of cheese, there could be several reasons for the surprising lack of impact on weight, though more research is needed. Cheese is fermented, meaning it has live bacterial cultures. That could have a positive effect on the gut microbiome, which appears to play a role in weight regulation. The fermentation process also creates vitamin K2, or menaquinone, which experimental studies have linked to improved insulin function. Insulin regulates blood sugar levels, hunger, calorie expenditure, and fat storage. (One upshot is that hard, aged cheeses, which are more fermented, probably provide more benefit than soft, less fermented ones.) There’s also some promising research about the benefits of a compound called the milk-fat globule membrane, which is intact in cheese but not in milk or butter.”

Read more (Wired)

Fermented dairy foods have been shown  to lower the risk of chronic diseases, inflammation and weight gain. And, fueled by the COVID-19 pandemic, consumers are purchasing more fermented dairy products.

“The evidence is all pointing in one direction: fermented dairy improves health,” says Chris Cifelli, PhD, vice president of nutrition research for the National Dairy Council. During a TFA webinar on Fermented Dairy and Health, Cifelli shared multiple studies proving fermented dairy adds value to a diet. “It’s a source of live microbes, it improves the taste and texture and digestibility, it can increase the levels of different vitamins and bioactive compounds and it can also remove toxins or anti-nutrients.”

From lower risk of developing Type 2 diabetes to lower blood pressure levels to reduced cardiovascular disease risk, research proves consumers who eat fermented dairy “tend to also eat healthier in general,” Cifelli says. “Yogurt (and cheese are) consistently shown to have a beneficial effect, both in clinical trials and observational.”

Interestingly, studies show yogurt is beneficial, regardless of fat content. Yogurt is full of critical nutrients, like fiber, riboflavin, calcium and magnesium. This “halo of health” surrounding yogurt has driven a recent sales surge.

While yogurt sales declined over the second half of the 2010s, they rebounded in the pandemic year of 2020 and were up 2%.

“Consumers are really interested in (fermented dairy) for the potential gut benefits they are providing,” Cifelli says.

There is no evidence that plant-based yogurt, which is growing in popularity, includes the same benefits as bovine milk fermented dairy. 

Kefir sales are on the rise;, too, are also growing. gGlobally, itkefir is expected to reach $1.84 billion in sales by 2027. Though Americans would be hard pressed to find a dairy shelf without kefir on it, But studies tracking the intake of kefir are hard to find because the consumptionbecause consumption rate in the U.S. is still low. Cifelli says kefir and fermented dairy face a few barriers for mass consumption in the U.S. 

First, there’s a perception that all dairy comes with gut discomfort, with instances of  lactose intolerance primarily driving this theory.

“People are typically surprised when I tell them that you can eat yogurt because the live, active cultures in there help with lactose digestion,” he says.

Second, consumers are nervous about hormones coming from cow products. But, Cifelli notes, all food has hormones. 

Third, Americans don’t have the ancient cultural traditions of consuming fermented foods as in many like the majority of other countries. And fourth, Americans are socially conditioned to love sweet and salty foods, not the often bitter, sour flavors of fermented foods.

“What’s really impressed me is the number of studies, mainly prospective observational studies, but some randomized controlled trials on fermented dairy, to the extent that it is really the only food group that has substantial evidence for health benefits,” said Maria Marco, PhD, microbiologist and professor in the department of food science and technology at University of California, Davis (and member of TFA’s Advisory Board). Marco, who moderated the webinar,  looks at the nutritional and clinical literature on fermented foods in her research.

Cifelli said this is because, in the U.S., milk and cheese have been actively consumed and studied for decades. The bulk of yogurt research is only from the last 20 years. Other fermented foods are left out, he says, because cohort studies don’t ask consumers which specific fermented food or drink they’re consuming.

“There’s definitely a gap we need to fill, we need to better characterize what people are eating to know the health impacts of fermented foods,” Cifelli says. “Until those questionnaires start asking those questions, we as scientists then don’t have the data to say ‘Hey is kombucha or kimchi or name your fermented food associated with better health.’”

The Science Behind Stinky Cheese

There’s a scientific reason behind the distinctly funky smells from cheese — it’s how microbes feed and communicate with each other. “What they’re saying has a lot to do with the delicious variety of flavors that cheese has to offer,” reads a statement from Tufts University, where the research was conducted. “The research team found that common bacteria essential to ripening cheese can sense and respond to compounds produced by fungi in the rind and released into the air, enhancing the growth of some species of bacteria over others. The composition of bacteria, yeast and fungi that make up the cheese microbiome is critical to flavor and quality of the cheese, so figuring out how that can be controlled or modified adds science to the art of cheese making.”

One of the authors of the study, Benjamin Wolfe, professor of biology at Tufts and TFA board member, said the research is noteworthy because “how these aromas impact the biology of the cheese microbiome had not been studied.” The findings will impact other fields, too.

Results were published in the journal Environmental Microbiology. The research was supported by a grant from the National Science Foundation.

Read more (Tufts University)

What is the Role of Cheese Starters?

Starters are one of the most critical steps in the cheese manufacturing process. An article in New Food Magazine lays out how a quality starter helps cheese ferment and create ideal coloring and flavor. Though cheese is an ancient food with a long history in many cultures, “we are still witnessing new strains coming to the fore[front] which can [be] implemented to achieve better flavor profiles and reduce ripening times.”

Read more (New Food Magazine)

Healthy Cheese?

“Cheese is finding new ground as a ‘health’ food,” writes John Lucey, professor of food science at the University of Wisconsin, Madison and the director of the Center for Dairy Research. Cheese has received a bad stereotype as a dairy food high in saturated fat and carbs, but Lucey notes cheese is high in vitamin C, riboflavin, vitamin B12 and folate. Studies show fermented cheeses reduce cancer rates, and fermented cheese contains bioactive peptides that reduce blood pressure, enhance the immune system and improve cardiovascular health.

Read more (Dairy Foods)

Scientists in Italy have discovered lactic acid bacteria in fermented food transfers to the gut microbiome. Though this is a widely accepted health benefit of fermented foods, there is little scientific research linking fermented food and the microbiome. The study looked at distribution of lactic acid bacteria (LAB) in humans based on location, age and lifestyle.

LAB genomes were reconstructed from about 300 foods and nearly 10,000 human fecal samples from humans from different continents. 
The most frequent LAB food in the human feces: streptococcus thermophilus and lactococcus lactis, commonly found in yogurt and cheese. 

“Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.”

Read more (Nature Communications)